The LMS determined the amino acid sequences of about 550 samples. About 270 of these analyses were for unknown proteins or peptides and the remainder were for quality control of synthetic peptides. Most of the unknown sequences determined were of endogenous peptides eluted from human MHC class I (LMS) and class II molecules. From these analyses, amino acid residues in peptides requisite for peptide binding to particular class I molecules have been determined. This information has been used to identify potential antigenic T cell epitopes that are recognized by cytotoxic and helper T lymphocytes. Knowledge of such epitopes is important for discerning diseases processes and of potential importance for vaccine development. Using such an approach several new antigenic epitopes recognized by T cells specific for influenza virus proteins and myelin basic proteins have been identified. In addition, proteins and peptides from a large variety of other sources have been sequenced by the facility: These include eosinophil derived proteins (H. Rosenberg, LHD); neutrophil p7 phox (T. Leto, LHD); Duffy antigen (C. Chitnis, LPD); malaria proteins (D. Kaslow, LPD); membrane antigen of basophilic cells (J.P. Kinet, MAIS); and Streptococcal Group B hyaluronate lyase, hippuricase and endopeptidase (D. Pritchard, Univ. of Alabama at Birmingham). Group B streptococci (GBS) are a major cause of serious human perinatal infections. Most clinical isolates of GBS secrete hyaluronate lyase, and production of high levels of the enzyme has been associated with strain virulence. Degenerate oligonucleotide primers, designed on the basis of the amino acid sequences of tryptic peptides prepared from the purified enzyme led to cloning of the gene from a lambda phage library of GBS chromosomal DNA fragments. When this gene was transformed into Escherichia coli, high level expression of hyaluronate lyase activity was obtained. A method was described by which a sequence-dependent peptide fingerprint can be rapidly obtained upon partial hydrolysis of peptide with hydrochloric acid and subsequent analysis by matrix assisted laser desorption/ionization mass spectrometry (MALDI-MS). When synthetic peptides are treated with 3M HCl for 5 min at 110 degrees C, amino acids are released in turn from the C-terminus or, depending on the peptide, from the N-terminus. Sequence information can be deduced by identifying the amino acid residue whose mass corresponds to the difference in MW between the major hydrolysis products, beginning from the MW of the starting peptide. The technique we have developed can be used to obtain a sequence-dependent "fingerprint" for a peptide cheaply and rapidly, starting with the picomole amounts of peptide, because the hydrolysate can be directly analyzed by MALDI-MS.